RetrogeneDB ID: retro_dord_732

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_67294:1186..2395(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Eif4a1
• Ensembl ID: ENSDORG00000014225
• Aliases: None
• Description: eukaryotic translation initiation factor 4A1 [Source:MGI Symbol;Acc:MGI:95303]

Sequence

>retro_dord_732
ATATCTTAGAGTCAGGATTCCCGATCCAGAGACAATGGCCCCGATGCGATGGAGCCAGAAGGTGTCATCGAGAGTAACTG
GAATGAAATTGTTGACAGCTTTGATGATATGAACCTTTCGGAGTCTCTCCTCCGTGGCATCTATGCCTATGGTTTTGAAA
AGCCCTCTGCCATCCAGCAACACACCATTCTTCCTTGTATCAAGGGTTATGAGGTGATCGCTCAAGCCCAATTTGGGACT
GGGAAAACAGCCACATTTGCCATATTGATTTTACAGCAGATTGAATTAGATCGAAAGGCCACTCAGGCCTTGGTCTTGGC
CCCCACTCGAGAATTAGCTCAGCAGATACAAAAAGTGGTCATGGCATTAGGAGATTATATGGGTGCTTCCTGTCATGCCT
GCATTGGGGGCACCAATGTACGTGCTGAAGTGCAGAAGTTGTAGATAGAAGCTCCCCATATCATCGTGGGTACTCCTGGC
CGTGTATTCGATATGCTTAATCGAAGATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGATGAAGCTGACGAGAT
GTTAAGCCGTGGGTTTAAGGACCAGATCTATGATATATTCCAAAAGCTCAACAGCAACACCCAGGTGGTCTTGTTGTCTG
CTACAATGCCTTCTGATGTGCTTGAGGTGACCAAGAAGTTCATGAGGGACCCCATTCGGATCCTTGTCAAGAAGGAAGAG
TTGACCCTGGAGGGTATCCGCCAATTCTACATCAATGTGGAAAGAGAGGAATGGAAGCTTGACACATTGTGTGACTTGTA
TGAAACCCTGACCATCGCTCAGGCAGTCATCTTCATCAACACCCGAAGGAAGGTCGACTGGCTTACTGAAAAGATGCATG
CCTGAGACTTCACAGTATCTGCCATGCATGGAGATATGGACCAAAAGGAACGAGATGTGATCATGAGGGAGTTCCGGTCT
GGCTCTAGCAGAGTACTGATTACCACTGACCTGCTGGCCAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTA
TGACCTTCCAACTAATAGGGAAAACTATATACACAGAATTGGTCGTGGTGGTCGTAAGGGTGTGGCTATTAATATGCTAA
CAGAAGAAAACAAGAGGACTCTTAGAGACATCAAGACCTTCTACAACACCTCCATTGAAGAAATGTCCCTCAATGTTGCA
GACCTCATC

Alignment

ORF - retro_dord_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          .S.SQDSRSRDNGPD.MEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQ..ILPCIKGY
Retrocopy IS*SQDSRSRDNGPDAMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQHTILPCIKGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQXXXXXXXXGDYMGASCHACIGGTNV
          .VIAQAQ.GTGKTATFAI.ILQQIELD.KATQALVLAPTRELAQQ........GDYMGASCHACIGGTNV
Retrocopy EVIAQAQFGTGKTATFAILILQQIELDRKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          RAEVQKL..EAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
Retrocopy RAEVQKL*IEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
          LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTI.QAVIFIN
Retrocopy LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTIAQAVIFIN

Parental  TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
          TRRKVDWLTEKMHA.DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
Retrocopy TRRKVDWLTEKMHA*DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP

Parental  TNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          TNRENYIHRIGRGGR...KGVAINM.TEE.KRTLRDI.TFYNTSIEEM.LNVADLI
Retrocopy TNRENYIHRIGRGGR---KGVAINMLTEENKRTLRDIKTFYNTSIEEMSLNVADLI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_732 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732 ,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,